[0;36mThank you for using runBioSimulations![0m

[0;36m================================================ Loading Singularity ================================================[0m

[0;36m=================================================== Set up storage ==================================================[0m

[0;36m========================================== Downloading COMBINE/OMEX archive =========================================[0m
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100 46637  100 46637    0     0  89699      0 --:--:-- --:--:-- --:--:-- 89699

[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================[0m
INFO:    Using cached SIF image
docker: Command recieved::<-i /root/archive.omex -o /root/outputs>
<-i>
Default case selected
VCell shall execute <biosimulations -i /root/archive.omex -o /root/outputs>
 INFO (CLIStandalone:38) - Starting Vcell... []{}
 INFO (PropertyLoader:578) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}
 INFO (PropertyLoader:584) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.37 []{}
 INFO (BiosimulationsCommand:98) - Beginning execution []{}
 INFO (CLIPythonManager:116) - Initializing Python... []{}
 INFO (CLIPythonManager:136) - Python initialization success! []{}
 INFO (ExecuteImpl:100) - Preparing output directory... []{}
ERROR (RunUtils:507) - java.lang.Exception: File '/root/outputs' could not be deleted! []{}
 INFO (ExecutionJob:86) - Executing OMEX archive /root/archive.omex []{}
-----------------------------------------------------------------------------------------------------
 INFO (NativeLib:29) - Loading combinej []{}
 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_c9fb41b9-99c7-4202-a7ce-95f8792c4e205109688810741472832 []{}
 INFO (SedmlJob:104) - Initializing SED-ML document... []{}
 WARN (SEDMLReader:249) - Unexpected [Element: <notes [Namespace: http://sed-ml.org/sed-ml/level1/version2]/>] []{}
 INFO (SedmlJob:117) - Processing SED-ML: VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml []{}
 INFO (SedmlJob:153) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  1 plot2D(s), and 0 plot3D(s)
 []{}
 INFO (SedmlJob:158) - Successful translation of SED-ML file : VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml []{}
-----------------------------------------------------------------------------------------------------
 INFO (SedmlJob:162) - Creating pseudo SED-ML for HDF5 conversion... []{}
 INFO (SedmlJob:174) - Creating Biomodel from pseudo SED-ML []{}
 INFO (SedmlJob:235) - Building solvers and starting simulation of all tasks...  []{}
 WARN (SEDMLReader:249) - Unexpected [Element: <notes [Namespace: http://sed-ml.org/sed-ml/level1/version2]/>] []{}
ERROR (SBMLImporter:1364) - unexpected assignment rule target 'SpeciesContext@50b1f030(id=null, name='Ca_c', species='Ca_c', structure='c', sbmlName='Ca_c')', adding as assignment rule - minimal support provided []{}
ERROR (SBMLImporter:1365) - need to create a VCLogger event []{}
 INFO (SBMLImporter:967) - adjustExpression(): replacing '___TIME_SYMBOL___' with 't' in (0.01 + (0.02 * ___TIME_SYMBOL___)) []{}
 INFO (SimulationContext:3205) - mathMapping: message = transforming the Rate Rules... []{}
 INFO (AbstractMathMapping:1451) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}
 INFO (AbstractMathMapping:1451) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}
 INFO (AbstractMathMapping:1451) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}
 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}
 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}
 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}
 INFO (SEDMLImporter:182) - Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}
taskToSimulationMap: 1
taskToListOfSubTasksMap: 1
taskToVariableMap: 1
topTaskToBaseTask: 1
 INFO (SolverHandler:422) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@68dd39d2 []{}
 INFO (SolverHandler:423) - Status: Finished: SOLVER_FINISHED:completed []{}
 INFO (SolverHandler:469) - Succesful execution: Model 'archive_VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml_PC12_clearance' Task 'Simulation42'. []{}
 INFO (SolverHandler:481) - Running simulation Simulation42, 329 ms []{}
-----------------------------------------------------------------------------------------------------
 INFO (SolverHandler:594) - Ran 1 simulation jobs for 1 biomodels. []{}
 INFO (SedmlJob:268) - Generating outputs...  []{}
 INFO (SedmlJob:322) - Generating CSV file...  []{}
 INFO (RunUtils:194) - Ignoring unsupported output `plot2d_Simulation42` while CSV generation. []{}
 INFO (RunUtils:200) - Generating report `report_Simulation42`. []{}
 INFO (RunUtils:380) - created csv file for report report_Simulation42: /root/outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/report_Simulation42.csv []{}
 INFO (RunUtils:200) - Generating report `__plot__plot2d_Simulation42`. []{}
 INFO (RunUtils:380) - created csv file for report __plot__plot2d_Simulation42: /root/outputs/VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml/__plot__plot2d_Simulation42.csv []{}
 INFO (SedmlJob:344) - Generating Plots...  []{}
 WARN (CLIPythonManager:78) - Using old style python invocation! []{}
 WARN (CLIPythonManager:250) - Temp out file didn't delete properly []{}
 WARN (CLIPythonManager:251) - Temp error file didn't delete properly []{}
 INFO (SedmlJob:356) - Generating HDF5 file...  []{}
 INFO (NonspatialResultsConverter:202) - Ignoring unsupported output `plot2d_Simulation42` while CSV generation. []{}
 INFO (SpatialResultsConverter:155) - Ignoring unsupported output `plot2d_Simulation42` while CSV generation. []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}
 INFO (SedmlJob:308) - Archiving result files []{}
 INFO (RunUtils:449) - Archiving resultant PDF files to `plots.zip`. []{}
 INFO (RunUtils:449) - Archiving resultant CSV files to `reports.zip`. []{}
 INFO (SedmlJob:315) - SED-ML : VCDB_27087758_Duman_JGenPhysiol_2008678691262362037853.sedml successfully completed []{}
 INFO (ExecutionJob:142) - Processing of SedML succeeded.
org.vcell.cli.run.SedmlStatistics@5cf8676a []{}
 INFO (NativeLib:29) - Loading jhdf5 []{}
 INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/root/outputs []{}
 INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}
 INFO (ExecutionJob:171) - Omex archive.omex processing completed (14s) []{}

[0;36m===================================================== Saving log ====================================================[0m
Completed 10.6 KiB/10.6 KiB (86.1 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/rawLog.txt
Completed 3.6 KiB/3.6 KiB (22.8 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/649b4bde642531fcf940a42a/outputs/log.yml

[0;36m================================================== Zipping outputs ==================================================[0m
  adding: outputs/ (stored 0%)
